Visualize HRR analysis results

Cells use the Homologous Recombination Repair (HRR) pathway to repair double-strand breaks generated as by-products of cellular metabolism, DNA replication errors, or exogenous factors.

Homologous Recombination Deficiency (HRD) is the inability of cells to repair double-strand DNA breaks using the HRR pathway.

The HRR visualization table summarizes relevant loss‑of‑function variants to provide information and enable assessment about likely biallelic variants in that gene, for example, BRCA1 and BRCA2. In addition, the HRR visualization table displays the cause and consequences of HRD by displaying metrics for measuring HRD (genomic loss-of-heterozygosity in the sample (%LOH), Genomic Instability Metric (GIM) score, and Genomic Instability Status).

Gene list for gene‑level LOH (Ion Reporter™ Software 5.14): ATM, BRCA1, BRCA2, BARD1, BRIP1, CDK12, CHEK1, CHEK2, FANCL, PALB2, RAD51B, RAD51C, RAD51D, and RAD54L.

Select one of the following options.

Option	Description
Visualize analysis results from an individual sample or from multiple samples simultaneously from the Analyses table.	In the Analyses table, select an individual sample result row, or select the checkbox next to each sample result that you want to visualize simultaneously, then click Visualize. Alternatively, click Actions Visualize.
Visualize analysis results individually from the Analysis Results screen.	In the Analyses table, click a sample result hyperlink in the Analysis column to open the Analysis Results, then click Visualize.

The Analysis Visualization opens to the TMB tab by default.

Select the HRR tab to review a summary of the analysis results about the genes and genomic alterations in the HRR pathway. For example, you can view information about genomic LOH (sample %LOH), CNVs, SNVs, INDELs and the Genomic Instability Metric (GIM). You can also view any exon-level deletions and duplications that are associated with BRCA1 and BRCA2 genes.
Note:
- If variants meeting a category are not detected, Not Detected is reported.
- You may see differences in variant calls reported in the Oncomine Variant tab or default variant table on the Analyses page and HRR summary table due to differences in the filter chain used and allele frequencies.
  - Variants in the HRR table are filtered using the TMB (Non-germline Mutations) filter chain. Variants in the default variants table are filtered using the Oncomine™ Extended filter chain (OEFC). OEFC retains pathogenic germline variants reported in ClinVar, whereas TMB (Non-germline Mutations) does not. As a result, the HRR summary table does not contain these variants.
  - Variants reported in HRR summary table have variant allele frequency ≥5%. As OEFC does not apply this criteria, all variant frequencies are reported in the default variant table.
Click DownloadCurrent Results TSV to download a tab-separated list of detected variants in the analysis results. Open the file with compatible software, such as Microsoft™ Excel™.

For more information about downloading files, see Download filtered variants.
Click DownloadFiltered Variants or DownloadAll Variants to download a ZIP folder of files that list the variants in the analysis results.

The file hrr_summary.tsv is included in the downloaded results.
Select the BRCA tab to visualize information about whole exon and multiple exon deletion in the BRCA1 and BRCA2 genes in somatic and germline samples with high sensitivity. For more information, see View Oncomine BRCA analysis results.
Select the IRGV & Generate Report tab, then click Generate Report to create and download a visualization report in PDF format, which includes the analysis results with graphs and metrics. For more information, see Create a visualization report.